A Brooklyn birthing facility fears it may have to close because of skyrocketing malpractice insurance rates which would leave the city with just one independent center for natural childbirth.

The Brooklyn Birthing Center says its insurance company has stopped covering midwives, and a costlier new policy could push them out of the baby-birthing business as well.

The news comes less than a week after the highly regarded Elizabeth Seton Childbearing Center, which delivers more than 400 babies a year, announced it will shut down its West 14th Street birthing rooms on Sept. 1 because of malpractice insurance costs it says have quadrupled.

“This could be the end of choice for women in New York,” said Katherine Abelson, director of the four-year-old Brooklyn center, which delivers about eight babies a month.

Owners of the Brooklyn Birthing Center, on Ocean Avenue, applied for a new insurance policy last week, but learned that the cost of insuring its two midwives could double.

“I don’t know if we’re going to be able to continue. This would make it very difficult to stay in business,” said Dr. Sol Neuhoff, an obstetrician-gynecologist who owns the center with two other doctors.

The city’s only other non-hospital birthing facility is the Morris Heights Childbearing Center in The Bronx, which employs five full-time midwives. That center is federally funded and insured, so is not in danger of closing.

But operators there are still alarmed by the malpractice crisis.

“It limits choices for women to have a low-risk delivery without drugs and other unnecessary medical intervention,” said the center’s executive director, Anita Wilenkin.

Midwife centers, which offer prenatal care and birthing rooms with homey furnishings, Jacuzzi tubs and kitchens, are also closing in New Jersey and other states hit by rising medical malpractice insurance rates.

Until recently, New Jersey had three independent birthing centers run by midwives. Last year, the last of the three closed.

Midwife Lonie Morris, who boasts more than 7,000 deliveries in 20 years, shut her Englewood, N.J., birth center after her malpractice rates jumped from $30,000 to $300,000 a year, she said. “I couldn’t pay my bills,’ ” she said.

Some insurance companies have dropped some types of high-risk coverage, including midwifery, since the 9/11 terror attacks. Others are quoting rates of $2 million to $4 million for a fraction of the coverage.